So, in this scene, Dexter goes to the marina where the yacht is usually docked, but finds it's space empty - the boat gone.

Needing to
know where it went (and whether Holly was on board), he distracts the
guard by setting off an alarm on a boat. He then sneaks into his office,
the security center for the marina, where the marina's video cameras
are monitored.

There, Dexter checks the recent security videos, and spots Travis sailing the Ricochet Rabbit out of the marina.

Checking the yacht's registration online, he learns the password to its GPS/tracking system ("Neptune"), then uses that password to find out where the yacht is.

He finds the Ricochet Rabbit later, docked at a secluded canal, near a bridge.

Q.
What is it actually in real life?

A. An office/storefront.

Q.
Where can I find it in real life?

A. This scene was shot at one of the office/storefronts at Pierpoint Landing, a small semi-circular concrete building located at 200 Aquarium Way, in Long Beach, CA.

That's just south of the Aquarium of the Pacific, at the far (southwest) corner of Rainbow Harbor.

Rainbow Harbor is home to a variety of large pleasure tour boats.
If you're looking to take a harbor tour, go whale watching, ride a tall
ship, or take a dinner cruise, this is the place to come. The area also
boasts a number of waterside restaurants.

This particular part of Rainbow Harbor, Pierpoint Landing,
specializes in sportsfishing. The small building there has a shop
selling bait, tackle, and snacks, as well as the City of Long Beach's
Rainbow Harbor office.

It appears that the guard's door, where Dexter enters, is located on the west end side of the small building.

That's just a few steps from the marina's dock #1. where they filmed the early Ricochet Rabbit scenes.

It's also just few yards west of the
sandy part of Shoreline Park, where they filmed the 3rd Season scene of
police discovering the body of the Skinner's second victim.

A. This was an easy one. I knew they had filmed the Ricochet Rabbit
scenes at the Rainbow Harbor dock right next to this Pierpoint Landing
building. And when the guard opens his door, you can see that dock just
outside the door. You can also see the circular swirl of the tile just
outside the door (part of the larger compass-pattern on the ground in
front of Pierpoint Landing). The position of a lone lamp post
allowed me to pinpoint the west side of the building as the side where
Dexter enters.